Variant report

Variant	rs6828639
Chromosome Location	chr4:45039597-45039598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10003954	0.82[ASN][1000 genomes]
rs10007392	0.84[ASN][1000 genomes]
rs10012579	0.83[ASN][1000 genomes]
rs10027158	0.82[ASN][1000 genomes]
rs10032137	0.81[ASN][1000 genomes]
rs10428432	0.82[ASN][1000 genomes]
rs10428433	0.82[ASN][1000 genomes]
rs10938387	0.82[ASN][1000 genomes]
rs11722695	0.84[ASN][1000 genomes]
rs11732028	0.84[ASN][1000 genomes]
rs12504429	0.84[ASN][1000 genomes]
rs12505216	0.84[ASN][1000 genomes]
rs12510234	0.82[ASN][1000 genomes]
rs12512251	0.81[ASN][1000 genomes]
rs12650122	0.84[ASN][1000 genomes]
rs12650843	0.84[ASN][1000 genomes]
rs13114648	0.80[ASN][1000 genomes]
rs13126186	0.82[ASN][1000 genomes]
rs13135680	0.81[ASN][1000 genomes]
rs13147324	0.83[ASN][1000 genomes]
rs13152342	0.82[ASN][1000 genomes]
rs1398264	0.84[ASN][1000 genomes]
rs1473819	0.88[ASN][1000 genomes]
rs1512304	0.84[ASN][1000 genomes]
rs1512310	0.81[ASN][1000 genomes]
rs1512311	0.81[ASN][1000 genomes]
rs1512312	0.81[ASN][1000 genomes]
rs1512324	0.84[ASN][1000 genomes]
rs1913018	0.84[ASN][1000 genomes]
rs28550246	0.80[ASN][1000 genomes]
rs28705704	0.84[ASN][1000 genomes]
rs34111600	0.83[ASN][1000 genomes]
rs34601600	0.81[ASN][1000 genomes]
rs4299625	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429758	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518285	0.84[ASN][1000 genomes]
rs4561959	0.84[ASN][1000 genomes]
rs4574450	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4588498	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4616793	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4974506	0.82[ASN][1000 genomes]
rs57883584	0.81[ASN][1000 genomes]
rs6447405	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447423	0.82[ASN][1000 genomes]
rs6447433	0.84[ASN][1000 genomes]
rs6814379	0.84[ASN][1000 genomes]
rs6817286	0.82[ASN][1000 genomes]
rs6842444	0.84[ASN][1000 genomes]
rs6845132	0.81[ASN][1000 genomes]
rs7356163	0.83[ASN][1000 genomes]
rs7671806	0.84[ASN][1000 genomes]
rs7672139	0.83[ASN][1000 genomes]
rs7680659	0.84[ASN][1000 genomes]
rs7682029	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686080	0.81[ASN][1000 genomes]
rs7686413	0.81[ASN][1000 genomes]
rs7693715	0.84[ASN][1000 genomes]
rs959904	0.97[ASN][1000 genomes]
rs969992	0.83[ASN][1000 genomes]
rs9917962	0.82[ASN][1000 genomes]
rs9991441	0.82[ASN][1000 genomes]
rs9999372	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531944	chr4:44299343-45200700	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1014327	chr4:44735209-45218149	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv878979	chr4:44871931-45102488	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2752047	chr4:44968572-45072206	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv878983	chr4:44982938-45039597	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6828639	GUF1	cis	parietal	SCAN
rs6828639	GUF1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:45038200-45039600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr4:45038200-45039600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:45038200-45040400	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr4:45038400-45039600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:45038400-45039800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:45038600-45039600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:45038600-45039800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr4:45038600-45039800	Enhancers	Fetal Heart	heart
9	chr4:45038600-45059000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:45039000-45039600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:45039200-45039600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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